Paracoccus denitrificans PD1222 Utilizes Hypotaurine via Transamination Followed by Spontaneous Desulfination To Yield Acetaldehyde and, Finally, Acetate for Growth

Felux, Ann-Katrin; Denger, Karin; Weiss, Michael J.; Cook, Alasdair M.; Schleheck, David

doi:10.1128/jb.00307-13

Cited by 14 publications

(9 citation statements)

References 56 publications

(62 reference statements)

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“…Taurine (2-aminoethanesulfonate) is a widespread natural product that can be used as an osmolyte and a source of energy, carbon, nitrogen or sulfur for growth by various bacteria ( Denger et al , 2004 , 2006; Weinitschke et al , 2007 ; Felux et al , 2013 ). Taurine can be synthesized (e.g.…”

Section: Resultsmentioning

confidence: 99%

“…This pathway is used for dissimilation of taurine as a carbon and nitrogen source, possibly serving also for sulfite detoxification and maintaining cell osmolarity ( Denger et al , 2004 ). The second pathway is used for utilization of taurine as a source of sulfur for aerobic growth and includes desulfonation of taurine to aminoacetaldehyde by dioxygenase TauD ( Denger et al , 2004 ; Felux et al , 2013 ).…”

Section: Resultsmentioning

confidence: 99%

“…Taurine utilization is described in many bacteria, for example Paracoccus denitrificans ( Felux et al , 2013 ), Ralstonia eutropha ( Weinitschke et al , 2007 ), Rhodobacter sphaeroides ( Denger et al , 2006 ) and Rhodococcus species ( Denger et al , 2004 ). TauR from the MocR subfamily was predicted and further experimentally confirmed to be a transcriptional activator of taurine metabolism ( Wiethaus et al , 2008 , Denger et al , 2004 , Mostafavi et al , 2014 ).…”

Section: Resultsmentioning

confidence: 99%

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Comparative genomics of pyridoxal 5′-phosphate-dependent transcription factor regulons in Bacteria

Suvorova

Rodionov

2016

Microbial Genomics

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The MocR-subfamily transcription factors (MocR-TFs) characterized by the GntR-family DNA-binding domain and aminotransferase-like sensory domain are broadly distributed among certain lineages of Bacteria. Characterized MocR-TFs bind pyridoxal 5′-phosphate (PLP) and control transcription of genes involved in PLP, gamma aminobutyric acid (GABA) and taurine metabolism via binding specific DNA operator sites. To identify putative target genes and DNA binding motifs of MocR-TFs, we performed comparative genomics analysis of over 250 bacterial genomes. The reconstructed regulons for 825 MocR-TFs comprise structural genes from over 200 protein families involved in diverse biological processes. Using the genome context and metabolic subsystem analysis we tentatively assigned functional roles for 38 out of 86 orthologous groups of studied regulators. Most of these MocR-TF regulons are involved in PLP metabolism, as well as utilization of GABA, taurine and ectoine. The remaining studied MocR-TF regulators presumably control genes encoding enzymes involved in reduction/oxidation processes, various transporters and PLP-dependent enzymes, for example aminotransferases. Predicted DNA binding motifs of MocR-TFs are generally similar in each orthologous group and are characterized by two to four repeated sequences. Identified motifs were classified according to their structures. Motifs with direct and/or inverted repeat symmetry constitute the majority of inferred DNA motifs, suggesting preferable TF dimerization in head-to-tail or head-to-head configuration. The obtained genomic collection of in silico reconstructed MocR-TF motifs and regulons in Bacteria provides a basis for future experimental characterization of molecular mechanisms for various regulators in this family.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

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Comparative genomics of pyridoxal 5′-phosphate-dependent transcription factor regulons in Bacteria

Suvorova

Rodionov

2016

Microbial Genomics

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“…Heterologous expression and purification of His tagged proteins. Heterolo go us expression of candidate genes and purification of the recombinant proteins were carried out according to our previously published protocol 25 • In brief, chro mosomal DNA was isolated using the lllustra bacteria genomicPrep Mini Spin Kit (GE Healthcare) and the target genes amplified by PCR using Phusion HF DNA Polymerase (Finnzymes) and the primer pairs given below. The PCR conditions the reactions were stopped by addition o f30% acetonitrile.…”

Section: Methodsmentioning

confidence: 99%

Sulphoglycolysis in Escherichia coli K-12 closes a gap in the biogeochemical sulphur cycle

Denger

Weiss

Felux

et al. 2014

Nature

Self Cite

118

215

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Sulphoquinovose (SQ, 6-deoxy-6-sulphoglucose) has been known for 50 years as the polar headgroup of the plant sulpholipid in the photosynthetic membranes of all higher plants, mosses, ferns, algae and most photosynthetic bacteria. It is also found in some non-photosynthetic bacteria, and SQ is part of the surface layer of some Archaea. The estimated annual production of SQ is 10,000,000,000 tonnes (10 petagrams), thus it comprises a major portion of the organo-sulphur in nature, where SQ is degraded by bacteria. However, despite evidence for at least three different degradative pathways in bacteria, no enzymic reaction or gene in any pathway has been defined, although a sulphoglycolytic pathway has been proposed. Here we show that Escherichia coli K-12, the most widely studied prokaryotic model organism, performs sulphoglycolysis, in addition to standard glycolysis. SQ is catabolised through four newly discovered reactions that we established using purified, heterologously expressed enzymes: SQ isomerase, 6-deoxy-6-sulphofructose (SF) kinase, 6-deoxy-6-sulphofructose-1-phosphate (SFP) aldolase, and 3-sulpholactaldehyde (SLA) reductase. The enzymes are encoded in a ten-gene cluster, which probably also encodes regulation, transport and degradation of the whole sulpholipid; the gene cluster is present in almost all (>91%) available E. coli genomes, and is widespread in Enterobacteriaceae. The pathway yields dihydroxyacetone phosphate (DHAP), which powers energy conservation and growth of E. coli, and the sulphonate product 2,3-dihydroxypropane-1-sulphonate (DHPS), which is excreted. DHPS is mineralized by other bacteria, thus closing the sulphur cycle within a bacterial community.

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“…The plasmids and bacterial strains used are listed in Table 1. P. denitrificans PD1222 was a gift from David Schleheck (34). Agrobacterium tumefaciens KYC55 was provided by Huiming Zheng (35).…”

Section: Methodsmentioning

confidence: 99%

Environmental Adaptability and Quorum Sensing: Iron Uptake Regulation during Biofilm Formation by Paracoccus denitrificans

Zhang

Gao

Wang

et al. 2018

Appl Environ Microbiol

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is a valuable model organism due to its versatile respiration capability and bioenergetic flexibility, both of which are critical to its survival in different environments. Quorum sensing (QS) plays a crucial role in the regulation of many cell functions; however, whether QS systems play a role in is unknown. In this study, we demonstrated that iron uptake systems in were directly regulated by a newly identified QS system. Genes coding for TonB-dependent systems, which transport chelated iron, were transcribed at higher levels in the QS-defective mutants. In contrast, genes coding for the Fbp system, which is TonB independent and transports unchelated ferric iron, were downregulated in the mutants. In brief, QS in triggers a switch in iron uptake from TonB-dependent to TonB-independent transport during biofilm formation as higher concentrations of iron accumulate in the exopolysaccharide (EPS). Switching from TonB-dependent iron uptake systems to TonB-independent systems not only prevents cells from absorbing excess iron but also conserves energy. Our data suggest that iron uptake strategies are directly regulated by QS in to support their survival in available ecological niches. As iron is an important trace metal for most organisms, its absorption is highly regulated. Fur has been reported as a prevalent regulator of iron acquisition. In addition, there is a relationship between QS and iron acquisition in pathogenic microbes. However, there have been few studies on the iron uptake strategies of nonpathogenic bacteria. In this study, we demonstrated that iron uptake systems in PD1222 were regulated by a newly identified PdeR/PdeI QS system during biofilm formation, and we put forward a hypothesis that QS-dependent iron uptake systems benefit the stability of biofilms. This report elaborates the correlation among QS, iron uptake, and biofilm formation and thus contributes to an understanding of the ecological behavior of environmental bacteria.

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Paracoccus denitrificans PD1222 Utilizes Hypotaurine via Transamination Followed by Spontaneous Desulfination To Yield Acetaldehyde and, Finally, Acetate for Growth

Cited by 14 publications

References 56 publications

Comparative genomics of pyridoxal 5′-phosphate-dependent transcription factor regulons in Bacteria

Comparative genomics of pyridoxal 5′-phosphate-dependent transcription factor regulons in Bacteria

Sulphoglycolysis in Escherichia coli K-12 closes a gap in the biogeochemical sulphur cycle

Environmental Adaptability and Quorum Sensing: Iron Uptake Regulation during Biofilm Formation by Paracoccus denitrificans

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